Align Inner-membrane translocator (characterized, see rationale)
to candidate BWI76_RS02805 BWI76_RS02805 sugar ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__Koxy:BWI76_RS02805 Length = 341 Score = 332 bits (851), Expect = 1e-95 Identities = 181/315 (57%), Positives = 232/315 (73%), Gaps = 6/315 (1%) Query: 61 RYLWP-----LLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMS 115 R+ WP ++AL ++L+ + + F+ + QD RL+GS IDILNR+APVALL+IGM+ Sbjct: 15 RFNWPKGMPQIIALLLVLVVDSLVAPHFYQVVLQDGRLFGSPIDILNRAAPVALLAIGMT 74 Query: 116 LVIATGGIDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLG 175 LVIATGGIDLSVGAVMAIAGA A++ V SL V+ A L G LAG NG LV+ L Sbjct: 75 LVIATGGIDLSVGAVMAIAGATAASMT-VAGHSLPIVLLASLGAGALAGLWNGILVAVLK 133 Query: 176 IQPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQ 235 IQP VATL+LMVAGRGVAQLI GQI+TF P A +G G L P PV I I L Sbjct: 134 IQPFVATLILMVAGRGVAQLITSGQIVTFDSPHLAWLGSGSLLLFPTPVIIAIVTLALFW 193 Query: 236 LLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDA 295 L RKTALG+FIEAVG N +A++ G+N + + + AY ++G+CAA+AG+I ADI+G+DA Sbjct: 194 LFTRKTALGMFIEAVGINIRAAKNAGVNTRVVVMLAYVLSGVCAAIAGIIVAADIRGADA 253 Query: 296 NNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIK 355 NNAGLWLELDA+LAVVIGG +L GGRF+L+LSVVGALIIQ + T I++SG P + N ++K Sbjct: 254 NNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPELNQVVK 313 Query: 356 AIVILTVLLLQSAKF 370 A+V+L VL++QS +F Sbjct: 314 AVVVLCVLIVQSPRF 328 Lambda K H 0.323 0.136 0.379 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 394 Number of extensions: 23 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 405 Length of database: 341 Length adjustment: 30 Effective length of query: 375 Effective length of database: 311 Effective search space: 116625 Effective search space used: 116625 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory